To understand the community structure and seasonal dynamics of gastrointestinal helminths of native fishes in Lake Chugutso, Tibet, four seasons of sampling investigation were conducted in September (Autumn) and December (winter) 2018, March (spring) and June (summer) 2019. Two native fish species, Gymnocypris waddellii and Triplophysa stewartii, were collected, which were different from the original records. Five different gastrointestinal helminths were found in G. waddellii, including Parabreviscolex niepini, Neoechinorhynchus sp., Alloclonium sp., Contracaecum sp., and Streptacera sp., Their morphological characteristics were described, and structure diagrams of some species were drawn. We found that the gastrointestinal helminth composition of G. waddellii in Chugusto Lake was regimal and most are widespread parasites, where birds play an important role in their transmission. The Shannon-Wiener diversity index for gastrointestinal helminths of G. waddellii was 0.70-1.27. Compared with the species number and diversity index of gastrointestinal helminths in lakes and reservoirs from other regions of China, they were relatively abundant species and showed a high community diversity, although there were fewer native fish species in Chugusto Lake. The Berger-Parker dominance index was 0.38-0.76, and nematodes were the dominant group. The numbers of nematode population dynamics showed certain seasonality:the highest abundance in autumn and lowest in summer, with a decrease in winter, and increase in spring. It is possible that the nematode population dynamics is related to water temperature, number of intermediate hosts, nematode life cycle, and fish host behavior during the breeding period. The infection rates of digenea, cestodes, and acanthocephalans were <10% in four seasons, and the mean abundance was also low. Freezing temperatures and hypothermia in winter may limit the number of intermediate host populations, and result in low infection rates and mean abundance of gastrointestinal parasites. No gastrointestinal helminths were found in T. stewartii, which was possibly related to the differences of gastrointestinal space size, food intake, and fish host habitat. The purpose of this study was to provide a theoretical basis for further understanding the parasite composition and characteristics in Tibet and the coevolution of parasites and fish hosts in the Qinghai Tibet Plateau.